tbuckley/cabot-search huggingface dataset:
Abstract 3983: Defining the role of FANCA in breast cancer development and cell cycle progression
Authors: Liang Luo, Wenjun Liu, Anna Palovcak, Fenghua Yuan, Fang Li, Daniel Calkins, Yan Li, Karoline Briegel, Daniel Bilbao, Evan Roberts, Christian Mason, Zhao-Jun Liu, Sylvia Daunert, Yanbin Zhang
Journal: Cancer Research (2023)

Abstract FANCA is one of the 22 known Fanconi anemia (FA) pathway genes and is indispensable for interstrand crosslink (ICL) repair. It is reported that FANCA is responsible for about 64% of FA cases and one important clinical characterization of FA patients is predisposition to cancer. However, analysis of TCGA database reveals that FANCA level is elevated in breast cancer patients, especially in ER- breast cancer, which is associated with the methylation status at the S-shore of CpG island ahead of FANCA gene. Moreover, the FANCA level is negatively correlated with the survival rate of breast cancer patients. To understand the implication of FANCA in breast cancer development, we have targeted FANCA by either CRISPR mediated knock-out (KO) or shRNA mediated knockdown (KD) in MDA-MB-231 breast cancer cells. Our data suggest that depletion of FANCA protein inhibits breast cancer growth both in vitro and in vivo. On the other hand, overexpressing FANCA in low-FANCA breast cancer cell line MDA-MB-468 promotes cancer cell proliferation. Cell cycle profiling reveals an inefficiency of MDA-MB-231 FANCA KO cells in G1 to S transition due to p21 and p27 upregulation in FANCA KO cells. In addition, the proliferation inefficiency in MDA-MB-231 FANCA KO cells is caused by Rb hypophosphorylation. Therefore, we conclude that FANCA contributes to the breast cancer development by promoting cell cycle progression through Rb/E2F signaling pathway. Our immunoprecipitation (IP) results indicate that in MDA-MB-231, FANCA is interacting with HES1, which is a transcription suppressor that binds to the promoter region of CDKN1A and CDKN1B to promote cell cycle progression, explaining how FANCA participates in cell cycle progression in breast cancer. Citation Format: Liang Luo, Wenjun Liu, Anna Palovcak, Fenghua Yuan, Fang Li, Daniel Calkins, Yan Li, Karoline Briegel, Daniel Bilbao, Evan Roberts, Christian Mason, Zhao-Jun Liu, Sylvia Daunert, Yanbin Zhang. Defining the role of FANCA in breast cancer development and cell cycle progression. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3983.
Abstract 5868: Uncovering key microenvironmental features for immunotherapy response at the subclonal level in pancreatic cancer
Authors: Er-Yen Yen, I-Lin Ho, Chieh-Yuan Li, Charles Dyke, Shan Jiang, Francesca Citron, Sergio Attanasio, Rutvi Shah, Ko-Chien Chen, Giulio Draetta, Andrea Viale
Journal: Cancer Research (2023)

Abstract The lack of suitable experimental approaches to investigate and model functional heterogeneity in vivo has had a profound negative impact on our understanding of how heterogeneity affects the response to immunotherapy. To bridge this technological gap, we leverage a new platform that visualizes the spatial architecture of subclones and microenvironments. To study heterogeneous populations of cells and their clonal dynamics in vivo, we performed barcode lineage tracing with next-generation sequencing analysis. It allows a quantitative evaluation of the spatial distribution and temporal clonal dynamic in vivo with multiple pharmacological perturbations, such as immune checkpoint blockade (ICB). We found that treatment with a PD1 inhibitor, despite a limited effect on tumor volume, induced dramatic changes in tumor clonal architecture. Furthermore, we revealed that subclones from well-defined geographical domains in vivo share differential behavior upon immune checkpoint blockade (ICB). By visualizing 40 different markers with multiplexed staining technology, we further identified that the microenvironment also exhibits a high level of spatial heterogeneity. Therefore, we coupled spatial barcode sequencing with high-content imaging and revealed the differential microenvironment feature of sensitive and resistant clones. We will further explore the mechanisms of immune evasion at the subclonal level. Through isolation and deep characterization of clonal lineages endowed with a distinct ability to engage the immune response, we hope to identify new vulnerabilities to overcome resistance to ICB. Citation Format: Er-Yen Yen, I-Lin Ho, Chieh-Yuan Li, Charles Dyke, Shan Jiang, Francesca Citron, Sergio Attanasio, Rutvi Shah, Ko-Chien Chen, Giulio Draetta, Andrea Viale. Uncovering key microenvironmental features for immunotherapy response at the subclonal level in pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5868.
Abstract 3604: Epithelial Caveolin-1 regulates lung metastasis in advanced stages of breast cancer
Authors: Dhirendra Pratap Singh, Rashmi Pathak, Abhishek Pandit, Philip J. Ebenezer, Nithya Jambunathan, Sanjay Kumar, Alexander Du Plooy, Joseph Francis, Mary E. White
Journal: Cancer Research (2023)

Abstract Organotypic metastasis is a well-orchestrated sequence of events that takes place in tumors. The interplay between secretory factors from the primary tumor and the microenvironment of a distant organ determines the fate of metastasis. A significant concern in effective triple-negative breast cancer (TNBC) treatment is lung metastasis. Caveolin-1 (Cav-1), a lipid raft protein, is an important component of the metastatic interplay and is reported to be upregulated in the advanced metastatic stage of breast cancer. Although Cav-1 has been shown to have oncogenic potential, its role in TNBC lung metastasis is not fully understood. Our data illustrates, knocking out Cav-1 in the 4T1 cells (a mouse breast cancer cell line) affects cell morphology, extracellular vesicle formation, and MMP release in vitro. Furthermore, a wound healing/cell migration assay showed reduced migration in Cav-1 KO 4T1 cells when compared to control 4T1 cells, and these findings were validated using Cav-1 siRNA. For investigating the metastatic role, we injected Cav-1 KO 4T1 and control 4T1 cells into the mammary fat pad of female BALB/c mice, a syngeneic mouse model of triple-negative breast cancer. We found no evidence of lung metastasis in Cav-1 KO 4T1 injected mice when compared to control 4T1 injected mice. This was further supported by mRNA profiling of the tumor. We observed 21 epithelial cell migration genes that are differentially expressed in Cav-1 KO tumors when compared to WT tumors. Correlation analysis from Breast Cancer Gene-Expression Miner v4.8 (bc-GenExMiner), a human database, showed a significant correlation between Cav-1 expression and several of the 21 epithelial cell migration genes, along with integrin 3 alpha (ITGα3). Interestingly, in silico protein docking predicted an interaction between Cav-1 and ITGα3, which was later confirmed by co-immunoprecipitation. The role of ITGα3 in metastasis was further corroborated by cell migration assay, which was affected when siRNA was used to silence ITGα3 gene expression. Collectively, these findings provide evidence that Cav-1 KO, along with ITGa3, plays an important role in distant lung metastasis in the 4T1 tumor-induced mice model. Citation Format: Dhirendra Pratap Singh, Rashmi Pathak, Abhishek Pandit, Philip J. Ebenezer, Nithya Jambunathan, Sanjay Kumar, Alexander Du Plooy, Joseph Francis, Mary E. White. Epithelial Caveolin-1 regulates lung metastasis in advanced stages of breast cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3604.
Abstract 3639: Impact of KRAS oncogenic signaling in tumorigenesis and immune evasion driven by extracellular vesicles (EVs)
Authors: Zulaida M. Soto Vargas, David C. Arteaga, Ikjot S. Sohal, Humna Hasan, Andrea L. Kasinski
Journal: Cancer Research (2023)

Abstract Mutations in Kristen rat sarcoma homolog (KRAS) occur in about 25% of cancers, making this protein one of the most frequently altered genes in cancer. KRAS mutations are not only associated with poor patient survival, but also with increased tumor aggressiveness and metastasis. Tumor development and metastasis are impacted by intercellular communication. Key mediators of cell-to-cell communication include vesicles secreted by cells, also known as extracellular vesicles (EVs). EVs released by cancer cells can mediate malignant transformation of non-cancerous cells as well as influence pre-metastatic niche formation. Conversely, inhibiting the secretion and release of EVs by cancer cells decreases tumor growth and metastasis. However, the mechanisms through which EVs drive tumorigenesis in KRAS mutant tumors are still understudied. Our lab recently reported that EVs from lung cancer cells drive invasion of non-tumorigenic lung epithelial cells. Here, we found that KRAS oncogenic signaling in the donor cells contributes to the EV-driven migration and invasion of non-tumorigenic lung epithelial cells. Previous studies have demonstrated that KRAS signaling drives immune evasion and promotes an “immune cold” tumor microenvironment. Our preliminary studies showed that EVs derived from KrasG12C lung cancer cells (H358) inhibit T cell proliferation and that blocking KRASG12C signaling, using ARS-1620 (KrasG12C inhibitor), impairs EV-driven T cell immunosuppression. We performed a comprehensive proteomic comparison between EVs isolated from H358 treated with ARS-1620 and those isolated from cells treated with DMSO (vehicle) and identified proteins involved in migration and invasion, such as LAMB-3, to be downregulated in EVs isolated from ARS-1620 treated cells. Ongoing studies aim to pinpoint the detailed mechanisms by which cancer cells utilize mutant KRAS signaling to promote loading of oncogenic cargo into EVs, and the resulting contributions to tumorigenesis and immune evasion. Citation Format: Zulaida M. Soto Vargas, David C. Arteaga, Ikjot S. Sohal, Humna Hasan, Andrea L. Kasinski. Impact of KRAS oncogenic signaling in tumorigenesis and immune evasion driven by extracellular vesicles (EVs). [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3639.
Abstract 2502: The role of high mobility group box-1 protein (HMGB1) in the microenvironment of non-small cell lung cancer
Authors: Tomohiro Habu, Keiichi Date, Ken Suzawa, Mao Yoshikawa, Masayoshi Ohki, Kazuma Iwata, Naoki Matsuda, Yin Min Thu, Kazuhiko Shien, Hiromasa Yamamoto, Shinichi Toyooka
Journal: Cancer Research (2023)

Abstract Introduction: The tumor microenvironment (TME) is critical in determining tumor development and progression. Among stromal cells in TME, cancer associated fibroblasts (CAFs) play a central role and are involved in various signals through their interaction with cancer cells in most solid tumors, leading to cancer progression and acquisition of drug resistance. Under these TME conditions, tumor cell death such as necrosis occurs, which in turn, results in the ectopic release of bioactive molecules collectively termed as damage-associated molecular patterns (DAMPs), which has been reported to play an important role in cancer progression. The purpose of this study is to clarify the effects of cancer cell-derived HMGB1, a representative DAMPs, on CAFs and to investigate whether it could be a potential therapeutic target. Methods: We established CAFs from resected non-small cell lung cancer (NSCLC) specimens and investigated the biological activity of HMGB1 on CAFs using in vitro co-culture models with NSCLC cell lines. Furthermore, we assessed the therapeutic efficacy of targeting cancer cell-derived HMGB1 using anti-HMGB1 neutralizing antibody. Results: Intracellular HMGB1 was expressed more in NSCLC cells than in normal bronchial epithelial cells and CAFs, and released from cancer cells extracellularly upon treatment with anticancer drugs. The stimulation with recombinant HMGB1 promoted the proliferation of CAFs in a dose-dependent manner, but not lung cancer cells. Co-culture with CAFs promoted cancer cells’ migratory ability and drug resistance, and stimulation with recombinant HMGB1 further enhanced these promoting effects, while administration of anti-HMGB1 neutralizing antibody suppressed these effects. On the other hand, these inhibitory effects were not observed in the absence of CAFs, suggestingHMGB1 has effect on CAFs, but not direct on cancer cells. Conclusion: HMGB1 plays an important role in cancer progression and acquisition of therapeutic resistance by upregulating the CAFs’ proliferation and activity and could be a therapeutic target in NSCLC. Citation Format: Tomohiro Habu, Keiichi Date, Ken Suzawa, Mao Yoshikawa, Masayoshi Ohki, Kazuma Iwata, Naoki Matsuda, Yin Min Thu, Kazuhiko Shien, Hiromasa Yamamoto, Shinichi Toyooka. The role of high mobility group box-1 protein (HMGB1) in the microenvironment of non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2502.
Abstract 137: Epigenetic regulation of APOBEC3A mutagenesis and tumor evolution during targeted therapy in non-small cell lung cancer
Authors: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Jessica Lin, Lecia Sequist, Zofia Piotrowska, Justin Gainor, Rémi Buisson, Michael Lawrence, Aaron Hata
Journal: Cancer Research (2023)

Abstract Acquired drug resistance to even the most effective anti-cancer targeted therapies remains an unsolved clinical problem. Although many drivers of acquired drug resistance have been identified, the underlying molecular mechanisms shaping tumor evolution during treatment are incompletely understood. We recently demonstrated that lung cancer targeted therapies commonly used in the clinic induce the expression of cytidine deaminase APOBEC3A (A3A), leading to sustained mutagenesis in drug tolerant cancer cells persisting during therapy. Preventing therapy-induced A3A mutagenesis by gene deletion decreased the accumulation of chromosomal aberrations and delayed the emergence of drug resistance. Thus, we hypothesize that inhibition of A3A may represent a potential therapeutic strategy to halt the evolution of resistant clones and prevent acquired resistance to lung cancer targeted therapies. Understanding the molecular mechanism of A3A induction during targeted therapy is a crucial step to develop targeting A3A therapies.Using a targeted drug combination screen, we found that DNA methyltransferase (DNMT) inhibitors induce expression of APOBEC3A in non-small cell lung cancer cells, phenocopying the effects of targeted therapies. RNA-seq profiling revealed that both targeted therapies and DNMT inhibitors increase expression of non-coding repeat RNAs. Repeatome analysis identified distinct classes of non-codding RNAs including endogenous retrovirus elements (ERV) in drug tolerant persister cells. Activation of endogenous intracellular viral sensing pathways by exogenous nucleic acids mimicking viral infection induced APOBEC3A, and genetic perturbation of RIG-I or MAVS reduced APOBEC3A induced by targeted therapy. These findings suggest that epigenetic derepression of retroviral repeat elements may underly APOBEC3A mutagenic activity and tumor evolution during lung cancer targeted therapy. Citation Format: Hideko Isozaki, Ramin Sakhtemani, Naveed Nikpour, Susanna Monroe, Jessica Lin, Lecia Sequist, Zofia Piotrowska, Justin Gainor, Rémi Buisson, Michael Lawrence, Aaron Hata. Epigenetic regulation of APOBEC3A mutagenesis and tumor evolution during targeted therapy in non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 137.
Abstract 5010: Inhibition of discoidin domain receptor 1 (DDR1) as a new therapeutic strategy for osteosarcoma
Authors: Jinglu Wang, Robert Walker, Francis Hornicek, Zhenfeng Duan
Journal: Cancer Research (2023)

Abstract Osteosarcoma is the most common type of bone cancer. Current management for osteosarcoma includes neoadjuvant chemotherapy and surgery. Unfortunately, some patients eventually develop recurrent or metastatic diseases and treatment options are extremely limited. Discoidin domain receptor 1 (DDR1) is a unique collagen-activated tyrosine kinase that participates in various human diseases, including cancer. DDR1 promotes the adhesion, proliferation, differentiation, migration, and metastasis of cancer cells. However, the expression and function of DDR1 remain unknown in osteosarcoma. The purpose of this study is to assess the expression, clinical prognostic relationship, and functional roles of DDR1 in osteosarcoma. The correlation between DDR1 expression in tumor tissues and clinicopathological features and prognosis was assessed via immunohistochemical staining of a unique tissue microarray (TMA) constructed from osteosarcoma specimens. Furthermore, DDR1 expression in osteosarcoma cell lines was determined by Western blot. DDR1-specific siRNA and a highly selective DDR1 inhibitor, 7rh, were applied to determine the impact of DDR1 expression on osteosarcoma cell growth and proliferation. In addition, the effect of DDR1 inhibition on clonogenicity was evaluated using a clonogenic assay, and a 3D cell culture model was used to mimic DDR1 effects in an in vivo environment. The results demonstrate that higher DDR1 expression significantly correlates with recurrence, metastasis, and shorter overall survival in osteosarcoma patients. The expression of DDR1 is also inversely correlated to the response to neoadjuvant chemotherapy. Therapeutically, DDR1 knockdown with siRNA or selective inhibition with 7rh decreases the proliferation and growth of osteosarcoma cells. In conclusion, our study supports DDR1 expression as an independent predictor of poor prognosis and a promising therapeutic target for osteosarcoma. Citation Format: Jinglu Wang, Robert Walker, Francis Hornicek, Zhenfeng Duan. Inhibition of discoidin domain receptor 1 (DDR1) as a new therapeutic strategy for osteosarcoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5010.
Nationwide Trends and Determinants of Germline BRCA1/2 Testing in Patients With Breast and Ovarian Cancer
Authors: Kelsey S. Lau-Min, Anne Marie McCarthy, Katherine L. Nathanson, Susan M. Domchek
Journal: Journal of the National Comprehensive Cancer Network (2023)

Germline genetic testing (GT) for BRCA1/2 is instrumental in identifying patients with breast and ovarian cancers who are eligible for PARP inhibitors (PARPi). Little is known about recent trends and determinants of GT since PARPi were approved for these patients.
Abstract 6520: Combination of serum human satellite RNA and miR-21 levels as a biomarker for diagnosis of pancreatic cancer
Authors: Takahiro Seimiya, Takahiro Kishikawa, Mtoyuki Otsuka, Mitsuhiro Fujishiro
Journal: Cancer Research (2023)

Abstract Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis due to the difficulty of its diagnosis. Because human satellite II (HSATII) RNA, a satellite repeat RNA, is highly and specifically expressed in human PDAC, the serum HSATII RNA level may be a biomarker for diagnosis of PDAC. To measure the serum HSATII RNA level with high sensitivity and reproducibility, we previously developed a convenient method, tandem repeat amplification by nuclease protection (TRAP) combined with droplet digital PCR (ddPCR). Here, we refined the original method by simultaneously measuring the serum miR-21 level to enhance the detection of PDAC. A total of 135 patients were enrolled in this study, including 65 patients with pancreatic cancer and 70 healthy controls. We developed the PDAC-Index as a combination of the HSATII RNA and miR-21 levels to discriminate PDAC from healthy controls. The PDAC-Index demonstrated good diagnostic performance (AUC: 0.92 (95% CI: 0.86-0.99); sensitivity: 0.94; specificity: 0.85) which was significantly better than HSATII RNA alone (AUC: 0.92 vs 0.82, p=0.004). Importantly, the PDAC-index was elevated in an early-stage PDAC case that was negative for CA19-9. The PDAC-index also discriminated PDAC from chronic pancreatitis and intraductal papillary mucinous neoplasm more accurately than CA19-9. These results suggest that the PDAC-Index may be a promising biomarker for diagnosis of PDAC. Citation Format: Takahiro Seimiya, Takahiro Kishikawa, Mtoyuki Otsuka, Mitsuhiro Fujishiro. Combination of serum human satellite RNA and miR-21 levels as a biomarker for diagnosis of pancreatic cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6520.